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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ), 'gf_id' => 'HOM05D001323', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001323' ), 'data_identifier' => 'HOM05D001323', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001323', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p37780' => 'bna', 'A05p36720' => 'bna', 'A07p24060' => 'bna', 'A07p27130' => 'bna', 'A08p00010' => 'bna', 'A09p22110' => 'bna', 'A09p60910' => 'bna', 'Aa31LG10G20' => 'aar', 'Aa31LG4G1570' => 'aar', 'Aa31LG9G6760' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.329' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.712' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1373' => 'aag', 'Actinidia00847' => 'ach', 'Actinidia04132' => 'ach', 'Actinidia12754' => 'ach', 'Actinidia17160' => 'ach', 'Actinidia33662' => 'ach', 'Actinidia33849' => 'ach', 'Actinidia40412' => 'ach', 'Ah.06g191530' => 'amhyb', 'Ah.09g231820' => 'amhyb', 'Ah.14g085630' => 'amhyb', 'AL1G28480' => 'aly', 'AL1G64540' => 'aly', 'AL2G40060' => 'aly', 'AL3G24420' => 'aly', 'AL8G12330' => 'aly', 'Aqoxy1G01674' => 'aox', 'Aqoxy3G04149' => 'aox', 'Aqoxy6G00337' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CZ09I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33JM38' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KDB7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GB6ZUZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H6YWDM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIM4ZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RK7M19' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T3X479' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TS9IG0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W20RPM' => 'arhy', 'AT1G16360' => 'ath', 'AT1G54320' => 'ath', 'AT1G79450' => 'ath', 'AT3G12740' => 'ath', 'AT5G46150' => 'ath', 'ATR0697G115' => 'atr', 'ATR0807G061' => 'atr', 'ATR1098G145' => 'atr', 'Atru.chr1.56' => 'acertr', 'Atru.chr10.1108' => 'acertr', 'Atru.chr12.1703' => 'acertr', 'Atru.chr7.1995' => 'acertr', 'AUR62004759' => 'cqu', 'AUR62037494' => 'cqu', 'AUR62037651' => 'cqu', 'AUR62041052' => 'cqu', 'BcaB02g07216' => 'bca', 'BcaB04g16905' => 'bca', 'BcaB04g18717' => 'bca', 'BcaB06g25516' => 'bca', 'BcaB07g30853' => 'bca', 'BcaB07g33160' => 'bca', 'BcaC01g04031' => 'bca', 'BcaC04g21729' => 'bca', 'BcaC05g29241' => 'bca', 'BcaC08g43685' => 'bca', 'BcaC08g45355' => 'bca', 'BcaC08g47506' => 'bca', 'BcaNung06214' => 'bca', 'BolC3t16860H' => 'bol', 'BolC3t21645H' => 'bol', 'BolC5t34185H' => 'bol', 'BolC6t36185H' => 'bol', 'BolC6t38149H' => 'bol', 'BolC7t43473H' => 'bol', 'BolC8t51997H' => 'bol', 'BolC9t55699H' => 'bol', 'BraA03t12933Z' => 'bra', 'BraA05t22476Z' => 'bra', 'BraA07t30054Z' => 'bra', 'BraA07t30358Z' => 'bra', 'BraA08t32057Z' => 'bra', 'BraA08t32058Z' => 'bra', 'BraA09t37816Z' => 'bra', 'BraA09t41464Z' => 'bra', 'C03p45850' => 'bna', 'C05p55170' => 'bna', 'C06p29870' => 'bna', 'C07p29310' => 'bna', 'C08p44510' => 'bna', 'C09p28240' => 'bna', 'CAN.G1602.2' => 'can', 'CAN.G269.8' => 'can', 'CAN.G90.8' => 'can', 'CANSAT35G1201' => 'cansat', 'CANSAT56G0617' => 'cansat', 'CARHR016830' => 'chi', 'CARHR045990' => 'chi', 'CARHR073110' => 'chi', 'CARHR087260' => 'chi', 'CARHR175650' => 'chi', 'Carub.0001s1610' => 'cru', 'Carub.0001s4485' => 'cru', 'Carub.0002s2631' => 'cru', 'Carub.0003s1210' => 'cru', 'Carub.0008s0177' => 'cru', 'Ca_01141_v3' => 'car', 'Ca_03108_v3' => 'car', 'Ca_03178_v3' => 'car', 'Ca_08289_v3' => 'car', 'Ca_23085_v3' => 'car', 'CBR_g12615' => 'cbr', 'CBR_g48129' => 'cbr', 'CBR_g6595' => 'cbr', 'CBR_g80039' => 'cbr', 'Cc00_g07350' => 'ccan', 'Cc03_g13970' => 'ccan', 'Cc05_g16550' => 'ccan', 'CDE02G3990' => 'cde', 'CDE05G1200' => 'cde', 'CDE05G1757' => 'cde', 'CDE11G0400' => 'cde', 'Cfa000911' => 'cfa', 'Cfa007747' => 'cfa', 'Cfa019372' => 'cfa', 'Ciclev10005291m.g' => 'ccl', 'Ciclev10012117m.g' => 'ccl', 'Ciclev10013434m.g' => 'ccl', 'Ciclev10015828m.g' => 'ccl', 'CiPaw.03G075900' => 'cil', 'CiPaw.04G049600' => 'cil', 'CiPaw.10G089400' => 'cil', 'CiPaw.11G057100' => 'cil', 'ClCG01G024820' => 'cla', 'ClCG02G018720' => 'cla', 'ClCG05G010500' => 'cla', 'COL.COLO4_16862' => 'col', 'COL.COLO4_24974' => 'col', 'COL.COLO4_26750' => 'col', 'COL.COLO4_31028' => 'col', 'COL.COLO4_38585' => 'col', 'COL.COLO4_38587' => 'col', 'Cpa.g.sc17.40' => 'cpa', 'Cpa.g.sc178.34' => 'cpa', 'Cpa.g.sc32.90' => 'cpa', 'Cre06.g278300' => 'cre', 'Cre07.g356750' => 'cre', 'CsaV3_3G018000' => 'csa', 'CsaV3_6G013450' => 'csa', 'CsaV3_6G051940' => 'csa', 'CSS0002142' => 'camsi', 'CSS0004327' => 'camsi', 'CSS0004928' => 'camsi', 'CSS0036073' => 'camsi', 'CSS0039031' => 'camsi', 'CSS0045656' => 'camsi', 'CSS0049670' => 'camsi', 'DCAR_007873' => 'dca', 'DCAR_008920' => 'dca', 'DCAR_009659' => 'dca', 'DCAR_010058' => 'dca', 'Dinv06070' => 'din', 'Dinv06072' => 'din', 'Dinv19574' => 'din', 'Dinv28247' => 'din', 'Dinv42462' => 'din', 'Duzib160G0766' => 'dzi', 'Duzib192G0570' => 'dzi', 'Duzib235G1032' => 'dzi', 'Duzib235G1158' => 'dzi', 'Duzib268G0322' => 'dzi', 'ECA233G4366' => 'eca', 'ECA233G4499' => 'eca', 'ECA236G0995' => 'eca', 'ECA240G3800' => 'eca', 'EL10Ac2g03298' => 'bvu', 'EL10Ac4g08912' => 'bvu', 'Eucgr.F04470' => 'egr', 'Eucgr.G00564' => 'egr', 'Eucgr.G00565' => 'egr', 'FAN11G0314' => 'fan', 'FAN11G1703' => 'fan', 'FAN16G3254' => 'fan', 'FAN16G3586' => 'fan', 'FAN19G1399' => 'fan', 'FAN21G0138' => 'fan', 'FAN21G2704' => 'fan', 'FAN23G1297' => 'fan', 'FAN25G1957' => 'fan', 'FAN25G2713' => 'fan', 'FAN26G2485' => 'fan', 'FAN28G2895' => 'fan', 'FAN28G3020' => 'fan', 'FvH4_1g27280' => 'fve', 'FvH4_3g05160' => 'fve', 'FvH4_3g14090' => 'fve', 'Glyma.08G163800' => 'gma', 'Glyma.08G234600' => 'gma', 'Glyma.09G090200' => 'gma', 'Glyma.13G356266' => 'gma', 'Glyma.15G017800' => 'gma', 'Glyma.15G212400' => 'gma', 'Glyma.15G263400' => 'gma', 'Glyma.16G038666' => 'gma', 'Glyma.16G038732' => 'gma', 'Glyma.19G114100' => 'gma', 'Gohir.A05G287500' => 'ghi', 'Gohir.A06G182800' => 'ghi', 'Gohir.A06G196400' => 'ghi', 'Gohir.A10G042950' => 'ghi', 'Gohir.A10G043100' => 'ghi', 'Gohir.D05G288700' => 'ghi', 'Gohir.D06G189600' => 'ghi', 'Gohir.D06G203900' => 'ghi', 'Gohir.D08G197233' => 'ghi', 'Gohir.D10G043950' => 'ghi', 'Gohir.D10G044100' => 'ghi', 'Gorai.007G242700' => 'gra', 'Gorai.009G303800' => 'gra', 'Gorai.010G222300' => 'gra', 'Gorai.010G237900' => 'gra', 'Gorai.011G046800' => 'gra', 'Gorai.011G047100' => 'gra', 'GSVIVG01012567001' => 'vvi', 'GSVIVG01021535001' => 'vvi', 'GSVIVG01036722001' => 'vvi', 'HanXRQChr01g0020601' => 'han', 'HanXRQChr03g0080301' => 'han', 'HanXRQChr04g0105561' => 'han', 'HanXRQChr05g0151661' => 'han', 'HanXRQChr07g0199001' => 'han', 'HanXRQChr09g0264471' => 'han', 'HanXRQChr11g0321971' => 'han', 'HanXRQChr12g0371201' => 'han', 'HanXRQChr13g0404361' => 'han', 'HanXRQChr13g0408881' => 'han', 'HanXRQChr17g0535781' => 'han', 'Haze_05644' => 'cav', 'Haze_07764' => 'cav', 'Haze_14326' => 'cav', 'Haze_26379' => 'cav', 'Hma1.2p1_0151F.1_g067020' => 'hma', 'Hma1.2p1_0158F.1_g069610' => 'hma', 'Hma1.2p1_0594F.1_g185920' => 'hma', 'HPP92_000992' => 'vpl', 'HPP92_000995' => 'vpl', 'HPP92_007246' => 'vpl', 'HPP92_013199' => 'vpl', 'Hund06864' => 'sun', 'Hund12030' => 'sun', 'Hund20122' => 'sun', 'Lalb_Chr03g0031891' => 'lal', 'Lalb_Chr08g0233471' => 'lal', 'Lalb_Chr19g0133171' => 'lal', 'Lalb_Chr20g0108431' => 'lal', 'Lalb_Chr24g0396011' => 'lal', 'Lalb_Chr25g0284371' => 'lal', 'Lj1g0006463' => 'lja', 'Lj2A10T41' => 'lonja', 'Lj2C321G7' => 'lonja', 'Lj2C511T3' => 'lonja', 'Lj3g0004086' => 'lja', 'Lj3g0012590' => 'lja', 'Lj3g0020989' => 'lja', 'Lj6g0007904' => 'lja', 'Lsat_1_v5_gn_1_91820' => 'lsa', 'Lsat_1_v5_gn_3_16240' => 'lsa', 'Lsat_1_v5_gn_3_67441' => 'lsa', 'Lsat_1_v5_gn_7_110961' => 'lsa', 'Lsat_1_v5_gn_7_69161' => 'lsa', 'Lsat_1_v5_gn_8_161180' => 'lsa', 'Manes.02G081400' => 'mes', 'Manes.03G079600' => 'mes', 'Manes.10G057000' => 'mes', 'Manes.17G073500' => 'mes', 'Mapoly0009s0074' => 'mpo', 'MBI02_g32906_MAGBIO' => 'mbi', 'MBI02_g32910_MAGBIO' => 'mbi', 'MBI02_g42528_MAGBIO' => 'mbi', 'MBI18_g01505_MAGBIO' => 'mbi', 'MCO06G254' => 'mco', 'MD05G1238200' => 'mdo', 'MD05G1280600' => 'mdo', 'MD09G1280100' => 'mdo', 'MD10G1216500' => 'mdo', 'MD17G1286800' => 'mdo', 'Medtr2g067760' => 'mtr', 'Medtr2g101400' => 'mtr', 'Medtr2g451450' => 'mtr', 'Medtr7g086110' => 'mtr', 'MELO3C007113.2' => 'cme', 'MELO3C019568.2' => 'cme', 'MELO3C019629.2' => 'cme', 'Migut.D02057' => 'egut', 'Migut.F00470' => 'egut', 'Migut.H01351' => 'egut', 'Migut.H01656' => 'egut', 'Migut.M01504' => 'egut', 'MSTRG.14789' => 'ama', 'MSTRG.16088' => 'ama', 'MSTRG.27192' => 'ama', 'MSTRG.7091' => 'ama', 'Nitab4.5_0000029g0170' => 'nta', 'Nitab4.5_0000914g0180' => 'nta', 'Nitab4.5_0002071g0020' => 'nta', 'Nitab4.5_0002297g0030' => 'nta', 'Nitab4.5_0002648g0010' => 'nta', 'Nitab4.5_0002862g0060' => 'nta', 'Nitab4.5_0024190g0010' => 'nta', 'Nn3g20439' => 'nnu', 'Nn4g24747' => 'nnu', 'Nn7g38367' => 'nnu', 'Oeu002793.1' => 'oeu', 'Oeu005063.1' => 'oeu', 'Oeu008945.1' => 'oeu', 'Oeu025999.1' => 'oeu', 'Oeu042525.1' => 'oeu', 'Oeu044191.1' => 'oeu', 'Oeu048995.1' => 'oeu', 'Os02g0173800' => 'osa', 'Os03g0120100' => 'osa', 'Os03g0785500' => 'osa', 'Os05g0529900' => 'osa', 'Os06g0665000' => 'osa', 'Os09g0560600' => 'osa', 'Peaxi162Scf00015g00243' => 'pax', 'Peaxi162Scf00045g02432' => 'pax', 'Peaxi162Scf00294g00616' => 'pax', 'Peaxi162Scf00452g00223' => 'pax', 'PGR031G2184' => 'pgr', 'PGR031G3297' => 'pgr', 'PGR042G1465' => 'pgr', 'PGSC0003DMG400021458' => 'stu', 'PGSC0003DMG400023414' => 'stu', 'Phvul.001G113400' => 'pvu', 'Phvul.005G048400' => 'pvu', 'Phvul.005G170000' => 'pvu', 'Phvul.009G212500' => 'pvu', 'Phvul.011G179200' => 'pvu', 'Potri.001G337466' => 'ptr', 'Potri.001G381500' => 'ptr', 'Potri.004G081100' => 'ptr', 'Potri.008G082100' => 'ptr', 'Potri.010G173900' => 'ptr', 'Potri.011G082100' => 'ptr', 'Potri.017G139300' => 'ptr', 'Pp3c15_15520' => 'ppa', 'Pp3c15_18239' => 'ppa', 'Pp3c1_36000' => 'ppa', 'Pp3c2_9840' => 'ppa', 'Pp3c7_3210' => 'ppa', 'PRCOL_00000284' => 'pco', 'PRCOL_00001843' => 'pco', 'Prupe.3G014200' => 'ppe', 'Prupe.4G084400' => 'ppe', 'Prupe.4G128200' => 'ppe', 'Psat0s3063g0160' => 'psa', 'Psat1g015320' => 'psa', 'Psat1g021120' => 'psa', 'Psat3g087600' => 'psa', 'Psat3g205920' => 'psa', 'Psat5g219920' => 'psa', 'Psat5g297240' => 'psa', 'Psat7g150320' => 'psa', 'PSO063G5684' => 'pso', 'PSO541G3353' => 'pso', 'PSO675G1091' => 'pso', 'PSO675G3921' => 'pso', 'PSO675G4102' => 'pso', 'PSO675G7858' => 'pso', 'PSO782G1577' => 'pso', 'QL02p064219' => 'qlo', 'QL04p093752' => 'qlo', 'QL05p055461' => 'qlo', 'RcHm_v2.0_Chr3g0488711' => 'rch', 'RcHm_v2.0_Chr5g0014591' => 'rch', 'RcHm_v2.0_Chr5g0023401' => 'rch', 'RcHm_v2.0_Chr6g0266591' => 'rch', 'Rhsim01G0006900' => 'rsi', 'Rhsim04G0003400' => 'rsi', 'Rhsim06G0244200' => 'rsi', 'Rhsim10G0185500' => 'rsi', 'Rhsim13G0116900' => 'rsi', 'Sabra08G0061100' => 'sbr', 'Sabra10G0133800' => 'sbr', 'Sabra11G0065400' => 'sbr', 'Sabra17G0117400' => 'sbr', 'SalBow4G0001' => 'sbo', 'SalBow7G0365' => 'sbo', 'SalBow7G1316' => 'sbo', 'SalBow8G0490' => 'sbo', 'SalBow8G1252' => 'sbo', 'SalBow8G4820' => 'sbo', 'Sc06g0003050' => 'sci', 'Sc09g0004560' => 'sci', 'Sc09g0007760' => 'sci', 'Sc24g0001640' => 'sci', 'Sed0000958' => 'sed', 'Sed0005631' => 'sed', 'Sed0011476' => 'sed', 'Sed0012056' => 'sed', 'Sed0015412' => 'sed', 'SEGI_13619' => 'sgi', 'SEGI_35077' => 'sgi', 'SGA_v2.0_scaffold186G40179' => 'sas', 'SGA_v2.0_scaffold49G18206' => 'sas', 'SGA_v2.0_scaffold51G18639' => 'sas', 'SGA_v2.0_scaffold543G52823' => 'sas', 'SMO358G0489' => 'smo', 'SMO361G0611' => 'smo', 'Solyc02g036440.3' => 'sly', 'Solyc05g054800.3' => 'sly', 'Sopen02g011790' => 'spe', 'Sopen05g033270' => 'spe', 'Sopen08g008610' => 'spe', 'Sp1g41860' => 'spa', 'Sp2g11010' => 'spa', 'Sp3g10900' => 'spa', 'Sp5g34500' => 'spa', 'TAR374G0566' => 'tar', 'TAR374G1194' => 'tar', 'TAR507G0002' => 'tar', 'TAR512G0001' => 'tar', 'TAR624G1096' => 'tar', 'THA.LOC104808137' => 'tha', 'THA.LOC104810274' => 'tha', 'THA.LOC104812384' => 'tha', 'THA.LOC104812867' => 'tha', 'THA.LOC104816993' => 'tha', 'Thecc.06G044000' => 'tca', 'Thecc.06G146300' => 'tca', 'Thecc.07G189300' => 'tca', 'Thhalv10000949m.g' => 'esa', 'Thhalv10011617m.g' => 'esa', 'Thhalv10018802m.g' => 'esa', 'Thhalv10021053m.g' => 'esa', 'TPR.G28186' => 'tpr', 'TPR.G28433' => 'tpr', 'TPR.G30650' => 'tpr', 'TPR.G30660' => 'tpr', 'TPR.G31224' => 'tpr', 'TPR.G37139' => 'tpr', 'TPR.G9408' => 'tpr', 'TWI38G0475' => 'twi', 'TWI59G0776' => 'twi', 'TWI73G1252' => 'twi', 'TWI74G0591' => 'twi', 'TWI77G0655' => 'twi', 'unitig_0.g1589' => 'ugi', 'unitig_37.g12194' => 'ugi', 'unitig_46.g18491' => 'ugi', 'unitig_748.g7611' => 'ugi', 'vmacro03354' => 'vma', 'vmacro05026' => 'vma', 'vmacro09765' => 'vma', 'vmacro09766' => 'vma', 'vmacro11680' => 'vma', 'vmacro15709' => 'vma', 'vmacro20464' => 'vma', 'vmacro22936' => 'vma', 'VMungo1080G0555' => 'vmu', 'VMungo1127G0163' => 'vmu', 'VMungo1309G2263' => 'vmu', 'VMungo1383G1033' => 'vmu', 'Zm00001eb001490' => 'zma', 'Zm00001eb059910' => 'zma', 'Zm00001eb207060' => 'zma', 'Zm00001eb233290' => 'zma', 'Zm00001eb274400' => 'zma', 'Zm00001eb293300' => 'zma', 'Zm00001eb319170' => 'zma', 'Zm00001eb320300' => 'zma', 'Zm00001eb389780' => 'zma' ) $gf_id = 'HOM05D001323' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001323' ) $data_identifier = 'HOM05D001323' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389780' $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